walk(K_plots, grid.arrange)
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
### TOTALN
walk(TOTALN_plots, grid.arrange)
lfmm_ind <-
lfmm_ind %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
filter(method == "ridge") %>%
filter(K_selection == "tracy.widom")
run_lmer(lfmm_ind, "TPRCOMBO", filepath = here(p4path, "LFMM_individual_TPR.csv"))
[[1]]
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | 0.0002 | 3.8849 | 3.8849 | 1 | 15.3180K | 374.16691 | 2.2 × 10−82*** |
| sampstrat | 0.1243 | 0.8737 | 0.2912 | 3 | 15.3180K | 28.04836 | 4.4 × 10−18*** |
| K | 0.0338 | 4.3713 | 4.3713 | 1 | 15.3180K | 421.01179 | 2.6 × 10−92*** |
| m | 0.0358 | 4.9147 | 4.9147 | 1 | 15.3180K | 473.35104 | 2.2 × 10−103*** |
| phi | 0.1114 | 47.5572 | 47.5572 | 1 | 15.3180K | 4580.39346 | 0.0*** |
| H | 0.1150 | 50.6577 | 50.6577 | 1 | 15.3180K | 4879.02098 | 0.0*** |
| r | −0.0183 | 1.2795 | 1.2795 | 1 | 15.3180K | 123.23782 | 1.6 × 10−28*** |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G | −0.0014 | 0.0023 | −0.5948 | 0.9336946 |
| EG - R | 0.0030 | 0.0023 | 1.2961 | 0.5653833 |
| EG - T*** | 0.0176 | 0.0023 | 7.5567 | 2.7 × 10−13*** |
| G - R | 0.0044 | 0.0023 | 1.8908 | 0.2319131 |
| G - T*** | 0.0190 | 0.0023 | 8.1508 | 5.0 × 10−14*** |
| R - T*** | 0.0146 | 0.0023 | 6.2616 | 2.3 × 10−9*** |
| *** p < 0.001 | ||||
run_lmer(lfmm_ind, "FDRCOMBO", filepath = here(p4path, "LFMM_individual_FDR.csv"))
[[1]]
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | −0.0027 | 549.7338 | 549.7338 | 1 | 15.3180K | 3196.9834256 | 0.0*** |
| sampstrat | 0.8382 | 16.4335 | 5.4778 | 3 | 15.3180K | 31.8563530 | 1.6 × 10−20*** |
| K | −0.0468 | 8.4059 | 8.4059 | 1 | 15.3180K | 48.8845389 | 2.8 × 10−12*** |
| m | −0.0687 | 18.1105 | 18.1105 | 1 | 15.3180K | 105.3216241 | 1.2 × 10−24*** |
| phi | −0.0317 | 3.8567 | 3.8567 | 1 | 15.3180K | 22.4287145 | 2.2 × 10−6*** |
| H | 0.0703 | 18.9143 | 18.9143 | 1 | 15.3180K | 109.9965860 | 1.2 × 10−25*** |
| r | −0.0029 | 0.0324 | 0.0324 | 1 | 15.3180K | 0.1886837 | 0.66 |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G | 0.0073 | 0.0095 | 0.7712 | 0.86748324 |
| EG - R*** | −0.0253 | 0.0095 | −2.6713 | 0.03788814*** |
| EG - T** | −0.0763 | 0.0095 | −8.0517 | 5.6 × 10−14** |
| G - R* | −0.0326 | 0.0095 | −3.4424 | 3.2 × 10−3* |
| G - T** | −0.0836 | 0.0095 | −8.8220 | 3.0 × 10−14** |
| R - T** | −0.0510 | 0.0095 | −5.3819 | 4.4 × 10−7** |
| *** p < 0.05 | ||||
| ** p < 0.001 | ||||
| * p < 0.01 | ||||
MEGAPLOT(lfmm_ind, "K.1", colpal = "turbo")
MEGAPLOT(lfmm_ind, "TPRCOMBO", colpal = "plasma")
MEGAPLOT(lfmm_ind, "FDRCOMBO", colpal = "viridis", direction = -1)
MEGAPLOT(lfmm_ind, "TOTALN", colpal = "viridis")
walk(K_plots, grid.arrange)
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
walk(TOTALN_plots, grid.arrange)
lfmm_ind_fullK <-
lfmm_ind_fullK %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
filter(method == "ridge")
run_lmer(lfmm_ind_fullK, "TPRCOMBO", filepath = here(p4path, "LFMM_indfullK_TPR.csv"))
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.
## [[1]]
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## </style>
## <table class="gt_table">
## <thead class="gt_header">
## <tr>
## <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
## </tr>
## <tr>
## <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
## </tr>
## </thead>
## <thead class="gt_col_headings">
## <tr>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">NumDF</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">F value</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Pr(>F)</th>
## </tr>
## </thead>
## <tbody class="gt_table_body">
## <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #FCFCFC; color: #000000;">0.0002</td>
## <td class="gt_row gt_right">2.2592</td>
## <td class="gt_row gt_right">2.2592</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">284.911850</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.4 × 10<sup class='gt_super'>−63</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0995</td>
## <td class="gt_row gt_right">0.2096</td>
## <td class="gt_row gt_right">0.0699</td>
## <td class="gt_row gt_right">3</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">8.812327</td>
## <td class="gt_row gt_right" style="font-weight: bold;">7.8 × 10<sup class='gt_super'>−6</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FEEADA; color: #000000;">0.0231</td>
## <td class="gt_row gt_right">2.0491</td>
## <td class="gt_row gt_right">2.0491</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">258.413832</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 × 10<sup class='gt_super'>−57</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FDD3AB; color: #000000;">0.0550</td>
## <td class="gt_row gt_right">11.5739</td>
## <td class="gt_row gt_right">11.5739</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">1459.604079</td>
## <td class="gt_row gt_right" style="font-weight: bold;">3.9 × 10<sup class='gt_super'>−305</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #FAC088; color: #000000;">0.0796</td>
## <td class="gt_row gt_right">24.2608</td>
## <td class="gt_row gt_right">24.2608</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">3059.565188</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #FABF85; color: #000000;">0.0814</td>
## <td class="gt_row gt_right">25.3972</td>
## <td class="gt_row gt_right">25.3972</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">3202.871668</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">r</td>
## <td class="gt_row gt_right" style="background-color: #EDEAFD; color: #000000;">−0.0148</td>
## <td class="gt_row gt_right">0.8346</td>
## <td class="gt_row gt_right">0.8346</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">105.249242</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.3 × 10<sup class='gt_super'>−24</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## </tbody>
##
## <tfoot class="gt_footnotes">
## <tr>
## <td class="gt_footnote" colspan="8"><sup class="gt_footnote_marks gt_asterisk">***</sup> p < 0.001</td>
## </tr>
## </tfoot>
## </table>
## </div>
##
## [[2]]
## <div id="tpzhtafrqn" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
## <style>html {
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##
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##
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##
## #tpzhtafrqn .gt_row {
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##
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##
## #tpzhtafrqn .gt_row_group_first td {
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## }
##
## #tpzhtafrqn .gt_summary_row {
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## padding-bottom: 8px;
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##
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##
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## text-align: right;
## font-variant-numeric: tabular-nums;
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##
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## font-weight: bold;
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##
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## font-style: italic;
## }
##
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## font-size: 65%;
## }
##
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## display: inline-block;
## line-height: 1em;
## text-align: right;
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## vertical-align: -0.25em;
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##
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##
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## </style>
## <table class="gt_table">
## <thead class="gt_header">
## <tr>
## <th colspan="5" class="gt_heading gt_title gt_font_normal" style>Tukey test</th>
## </tr>
## <tr>
## <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
## </tr>
## </thead>
## <thead class="gt_col_headings">
## <tr>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Estimate</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Z ratio</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">p</th>
## </tr>
## </thead>
## <tbody class="gt_table_body">
## <tr><td class="gt_row gt_left">EG - G</td>
## <td class="gt_row gt_right" style="background-color: #EAE6FD; color: #000000;">−0.0017</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">−0.8564</td>
## <td class="gt_row gt_right">0.8272429</td></tr>
## <tr><td class="gt_row gt_left">EG - R</td>
## <td class="gt_row gt_right" style="background-color: #FDF6F0; color: #000000;">0.0008</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">0.3925</td>
## <td class="gt_row gt_right">0.9794972</td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - T<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #FABF85; color: #000000;">0.0080</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">3.9129</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.3 × 10<sup class='gt_super'>−4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left">G - R</td>
## <td class="gt_row gt_right" style="background-color: #FEE8D5; color: #000000;">0.0025</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">1.2489</td>
## <td class="gt_row gt_right">0.5956070</td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">G - T<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0097</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">4.7687</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 × 10<sup class='gt_super'>−5</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">R - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #FBC590; color: #000000;">0.0072</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">3.5208</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.4 × 10<sup class='gt_super'>−3</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
## </tbody>
##
## <tfoot class="gt_footnotes">
## <tr>
## <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p < 0.001</td>
## </tr>
## <tr>
## <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">**</sup> p < 0.01</td>
## </tr>
## </tfoot>
## </table>
## </div>
run_lmer(lfmm_ind_fullK, "FDRCOMBO", filepath = here(p4path, "LFMM_indfullK_FDR.csv"))
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.
## [[1]]
## <div id="fixjlqekcp" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
## <style>html {
## font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Helvetica Neue', 'Fira Sans', 'Droid Sans', Arial, sans-serif;
## }
##
## #fixjlqekcp .gt_table {
## display: table;
## border-collapse: collapse;
## margin-left: auto;
## margin-right: auto;
## color: #333333;
## font-size: 16px;
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## font-style: normal;
## background-color: #FFFFFF;
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## border-top-style: solid;
## border-top-width: 2px;
## border-top-color: #A8A8A8;
## border-right-style: none;
## border-right-width: 2px;
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## border-bottom-style: solid;
## border-bottom-width: 2px;
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## border-left-style: none;
## border-left-width: 2px;
## border-left-color: #D3D3D3;
## }
##
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## background-color: #FFFFFF;
## text-align: center;
## border-bottom-color: #FFFFFF;
## border-left-style: none;
## border-left-width: 1px;
## border-left-color: #D3D3D3;
## border-right-style: none;
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## color: #333333;
## font-size: 125%;
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## padding-top: 4px;
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## color: #333333;
## font-size: 85%;
## font-weight: initial;
## padding-top: 0;
## padding-bottom: 6px;
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## border-top-width: 0;
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## border-bottom-style: solid;
## border-bottom-width: 2px;
## border-bottom-color: #D3D3D3;
## }
##
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## border-top-style: solid;
## border-top-width: 2px;
## border-top-color: #D3D3D3;
## border-bottom-style: solid;
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## border-left-style: none;
## border-left-width: 1px;
## border-left-color: #D3D3D3;
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## border-right-width: 1px;
## border-right-color: #D3D3D3;
## }
##
## #fixjlqekcp .gt_col_heading {
## color: #333333;
## background-color: #FFFFFF;
## font-size: 100%;
## font-weight: normal;
## text-transform: inherit;
## border-left-style: none;
## border-left-width: 1px;
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## border-right-style: none;
## border-right-width: 1px;
## border-right-color: #D3D3D3;
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## padding-top: 5px;
## padding-bottom: 6px;
## padding-left: 5px;
## padding-right: 5px;
## overflow-x: hidden;
## }
##
## #fixjlqekcp .gt_column_spanner_outer {
## color: #333333;
## background-color: #FFFFFF;
## font-size: 100%;
## font-weight: normal;
## text-transform: inherit;
## padding-top: 0;
## padding-bottom: 0;
## padding-left: 4px;
## padding-right: 4px;
## }
##
## #fixjlqekcp .gt_column_spanner_outer:first-child {
## padding-left: 0;
## }
##
## #fixjlqekcp .gt_column_spanner_outer:last-child {
## padding-right: 0;
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##
## #fixjlqekcp .gt_group_heading {
## padding-top: 8px;
## padding-bottom: 8px;
## padding-left: 5px;
## padding-right: 5px;
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## background-color: #FFFFFF;
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## font-weight: initial;
## text-transform: inherit;
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## border-left-style: none;
## border-left-width: 1px;
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## border-right-width: 1px;
## border-right-color: #D3D3D3;
## vertical-align: middle;
## }
##
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## <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
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## <tr>
## <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
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## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
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## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
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## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
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## <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #FCFBFC; color: #000000;">−0.0025</td>
## <td class="gt_row gt_right">501.9981</td>
## <td class="gt_row gt_right">501.9981</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">3776.700755</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.5655</td>
## <td class="gt_row gt_right">14.8749</td>
## <td class="gt_row gt_right">4.9583</td>
## <td class="gt_row gt_right">3</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">37.302920</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.2 × 10<sup class='gt_super'>−24</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FDF9F6; color: #000000;">0.0220</td>
## <td class="gt_row gt_right">1.8480</td>
## <td class="gt_row gt_right">1.8480</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">13.902783</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.9 × 10<sup class='gt_super'>−4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FEF2E9; color: #000000;">0.0711</td>
## <td class="gt_row gt_right">19.3767</td>
## <td class="gt_row gt_right">19.3767</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">145.777616</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.1 × 10<sup class='gt_super'>−33</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #F6F5FC; color: #000000;">−0.0329</td>
## <td class="gt_row gt_right">4.1374</td>
## <td class="gt_row gt_right">4.1374</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">31.127031</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.5 × 10<sup class='gt_super'>−8</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #FEEFE2; color: #000000;">0.0974</td>
## <td class="gt_row gt_right">36.3261</td>
## <td class="gt_row gt_right">36.3261</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">273.293640</td>
## <td class="gt_row gt_right" style="font-weight: bold;">7.3 × 10<sup class='gt_super'>−61</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">r</td>
## <td class="gt_row gt_right" style="background-color: #FAF9FC; color: #000000;">−0.0122</td>
## <td class="gt_row gt_right">0.5737</td>
## <td class="gt_row gt_right">0.5737</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">4.316443</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.038<sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
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## </style>
## <table class="gt_table">
## <thead class="gt_header">
## <tr>
## <th colspan="5" class="gt_heading gt_title gt_font_normal" style>Tukey test</th>
## </tr>
## <tr>
## <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
## </tr>
## </thead>
## <thead class="gt_col_headings">
## <tr>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Estimate</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Z ratio</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">p</th>
## </tr>
## </thead>
## <tbody class="gt_table_body">
## <tr><td class="gt_row gt_left">EG - G</td>
## <td class="gt_row gt_right" style="background-color: #FCFAF7; color: #000000;">0.0024</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">0.2905</td>
## <td class="gt_row gt_right">0.991466</td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - R<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #D2CCFD; color: #000000;">−0.0306</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">−3.6725</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.4 × 10<sup class='gt_super'>−3</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #8C8AFC; color: #000000;">−0.0748</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">−8.9768</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.7 × 10<sup class='gt_super'>−14</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">G - R<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #CFC8FD; color: #000000;">−0.0330</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">−3.9628</td>
## <td class="gt_row gt_right" style="font-weight: bold;">4.3 × 10<sup class='gt_super'>−4</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">G - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #8787FC; color: #000000;">−0.0772</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">−9.2667</td>
## <td class="gt_row gt_right" style="font-weight: bold;">4.3 × 10<sup class='gt_super'>−14</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">R - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #BEB7FD; color: #000000;">−0.0442</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">−5.3064</td>
## <td class="gt_row gt_right" style="font-weight: bold;">6.7 × 10<sup class='gt_super'>−7</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
## </tbody>
##
## <tfoot class="gt_footnotes">
## <tr>
## <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p < 0.01</td>
## </tr>
## <tr>
## <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">**</sup> p < 0.001</td>
## </tr>
## </tfoot>
## </table>
## </div>
walk(K_plots, grid.arrange)
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
walk(TOTALN_plots, grid.arrange)
lfmm_site <-
lfmm_site %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
filter(method == "ridge") %>%
filter(K_selection == "tracy.widom")
run_lmer(lfmm_site, "TPRCOMBO", filepath = here(p4path, "LFMM_site_TPR.csv"))
[[1]]
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | −0.0004 | 0.0593 | 0.0593 | 1 | 8.6090K | 8.070827 | 4.5 × 10−3*** |
| sampstrat | 0.0362 | 0.1180 | 0.0590 | 2 | 8.6090K | 8.023909 | 3.3 × 10−4** |
| K | 0.0160 | 0.5507 | 0.5507 | 1 | 8.6090K | 74.893340 | 5.9 × 10−18** |
| m | 0.0417 | 3.7529 | 3.7529 | 1 | 8.6090K | 510.419793 | 7.7 × 10−110** |
| phi | 0.0536 | 6.1900 | 6.1900 | 1 | 8.6090K | 841.869068 | 1.1 × 10−176** |
| H | 0.0741 | 11.8217 | 11.8217 | 1 | 8.6090K | 1607.807275 | 1.7 × 10−322** |
| r | −0.0213 | 0.9766 | 0.9766 | 1 | 8.6090K | 132.822293 | 1.7 × 10−30** |
| *** p < 0.01 | |||||||
| ** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ | 0.0043 | 0.0023 | 1.8813 | 0.14407422 |
| EG - R*** | 0.0091 | 0.0023 | 4.0035 | 1.8 × 10−4*** |
| EQ - R | 0.0048 | 0.0023 | 2.1241 | 0.08499688 |
| *** p < 0.001 | ||||
run_lmer(lfmm_site, "FDRCOMBO", filepath = here(p4path, "LFMM_site_FDR.csv"))
[[1]]
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | −0.0083 | 25.3129 | 25.3129 | 1 | 8.6110K | 842.37960203 | 8.7 × 10−177*** |
| sampstrat | 1.0906 | 0.0540 | 0.0270 | 2 | 8.6110K | 0.89778252 | 0.410 |
| K | 0.0096 | 0.1966 | 0.1966 | 1 | 8.6110K | 6.54282626 | 0.011** |
| m | 0.0161 | 0.5617 | 0.5617 | 1 | 8.6110K | 18.69390804 | 1.6 × 10−5*** |
| phi | −0.0238 | 1.2192 | 1.2192 | 1 | 8.6110K | 40.57304948 | 2.0 × 10−10*** |
| H | 0.0009 | 0.0018 | 0.0018 | 1 | 8.6110K | 0.06058928 | 0.810 |
| r | 0.0036 | 0.0281 | 0.0281 | 1 | 8.6110K | 0.93373450 | 0.330 |
| *** p < 0.001 | |||||||
| ** p < 0.05 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ | −0.0061 | 0.0046 | −1.3303 | 0.3782653 |
| EG - R | −0.0024 | 0.0046 | −0.5263 | 0.8584367 |
| EQ - R | 0.0037 | 0.0046 | 0.8037 | 0.7007541 |
MEGAPLOT(lfmm_site, "K.1", colpal = "turbo")
MEGAPLOT(lfmm_site, "TPRCOMBO", colpal = "plasma")
MEGAPLOT(lfmm_site, "FDRCOMBO", colpal = "viridis", direction = -1)
MEGAPLOT(lfmm_site, "TOTALN", colpal = "viridis")
walk(K_plots, grid.arrange)
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
walk(TOTALN_plots, grid.arrange)
lfmm_site_fullK <-
lfmm_site_fullK %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
filter(method == "ridge")
run_lmer(lfmm_site_fullK, "TPRCOMBO", filepath = here(p4path, "LFMM_sitefullK_TPR.csv"))
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.
## [[1]]
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## <table class="gt_table">
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## <tr>
## <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
## </tr>
## <tr>
## <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
## </tr>
## </thead>
## <thead class="gt_col_headings">
## <tr>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">NumDF</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">F value</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Pr(>F)</th>
## </tr>
## </thead>
## <tbody class="gt_table_body">
## <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #F9F9FC; color: #000000;">−0.0018</td>
## <td class="gt_row gt_right">1.1952</td>
## <td class="gt_row gt_right">1.1952</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">183.240394</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.5 × 10<sup class='gt_super'>−41</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #FEE6D1; color: #000000;">0.0191</td>
## <td class="gt_row gt_right">0.0892</td>
## <td class="gt_row gt_right">0.0446</td>
## <td class="gt_row gt_right">2</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">6.835991</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 × 10<sup class='gt_super'>−3</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FEEBDA; color: #000000;">0.0152</td>
## <td class="gt_row gt_right">0.4970</td>
## <td class="gt_row gt_right">0.4970</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">76.192821</td>
## <td class="gt_row gt_right" style="font-weight: bold;">3.1 × 10<sup class='gt_super'>−18</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FDD0A5; color: #000000;">0.0389</td>
## <td class="gt_row gt_right">3.2589</td>
## <td class="gt_row gt_right">3.2589</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">499.649532</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.3 × 10<sup class='gt_super'>−107</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #FCCA9A; color: #000000;">0.0442</td>
## <td class="gt_row gt_right">4.2123</td>
## <td class="gt_row gt_right">4.2123</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">645.825647</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.9 × 10<sup class='gt_super'>−137</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0656</td>
## <td class="gt_row gt_right">9.2807</td>
## <td class="gt_row gt_right">9.2807</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">1422.900812</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.6 × 10<sup class='gt_super'>−288</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">r</td>
## <td class="gt_row gt_right" style="background-color: #DBD6FD; color: #000000;">−0.0206</td>
## <td class="gt_row gt_right">0.9155</td>
## <td class="gt_row gt_right">0.9155</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">140.355642</td>
## <td class="gt_row gt_right" style="font-weight: bold;">4.0 × 10<sup class='gt_super'>−32</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## </tbody>
##
## <tfoot class="gt_footnotes">
## <tr>
## <td class="gt_footnote" colspan="8"><sup class="gt_footnote_marks gt_asterisk">***</sup> p < 0.001</td>
## </tr>
## <tr>
## <td class="gt_footnote" colspan="8"><sup class="gt_footnote_marks gt_asterisk">**</sup> p < 0.01</td>
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## <th colspan="5" class="gt_heading gt_title gt_font_normal" style>Tukey test</th>
## </tr>
## <tr>
## <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
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## <thead class="gt_col_headings">
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## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Estimate</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
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## <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - EQ<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #FBC48F; color: #000000;">0.0057</td>
## <td class="gt_row gt_right">0.0021</td>
## <td class="gt_row gt_right">2.6691</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.02077436<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - R<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0076</td>
## <td class="gt_row gt_right">0.0021</td>
## <td class="gt_row gt_right">3.5508</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 × 10<sup class='gt_super'>−3</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
## <tr><td class="gt_row gt_left">EQ - R</td>
## <td class="gt_row gt_right" style="background-color: #FEE9D7; color: #000000;">0.0019</td>
## <td class="gt_row gt_right">0.0021</td>
## <td class="gt_row gt_right">0.8835</td>
## <td class="gt_row gt_right">0.65075396</td></tr>
## </tbody>
##
## <tfoot class="gt_footnotes">
## <tr>
## <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p < 0.05</td>
## </tr>
## <tr>
## <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">**</sup> p < 0.01</td>
## </tr>
## </tfoot>
## </table>
## </div>
run_lmer(lfmm_site_fullK, "FDRCOMBO", filepath = here(p4path, "LFMM_sitefullK_FDR.csv"))
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.
## [[1]]
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## <tr>
## <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
## </tr>
## <tr>
## <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
## </tr>
## </thead>
## <thead class="gt_col_headings">
## <tr>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">NumDF</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">F value</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Pr(>F)</th>
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## <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #FAFAFC; color: #000000;">−0.0187</td>
## <td class="gt_row gt_right">129.4249</td>
## <td class="gt_row gt_right">129.4249</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">1992.658631</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">1.2219</td>
## <td class="gt_row gt_right">2.3866</td>
## <td class="gt_row gt_right">1.1933</td>
## <td class="gt_row gt_right">2</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">18.372105</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 × 10<sup class='gt_super'>−8</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FCFBFA; color: #000000;">0.0190</td>
## <td class="gt_row gt_right">0.7755</td>
## <td class="gt_row gt_right">0.7755</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">11.939477</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.5 × 10<sup class='gt_super'>−4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FCFBFA; color: #000000;">0.0196</td>
## <td class="gt_row gt_right">0.8298</td>
## <td class="gt_row gt_right">0.8298</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">12.776418</td>
## <td class="gt_row gt_right" style="font-weight: bold;">3.5 × 10<sup class='gt_super'>−4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #FAFAFC; color: #000000;">−0.0191</td>
## <td class="gt_row gt_right">0.7830</td>
## <td class="gt_row gt_right">0.7830</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">12.054888</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.2 × 10<sup class='gt_super'>−4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #FCFAF7; color: #000000;">0.0389</td>
## <td class="gt_row gt_right">3.2570</td>
## <td class="gt_row gt_right">3.2570</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">50.145685</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.5 × 10<sup class='gt_super'>−12</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left">r</td>
## <td class="gt_row gt_right" style="background-color: #FCFCFB; color: #000000;">0.0065</td>
## <td class="gt_row gt_right">0.0916</td>
## <td class="gt_row gt_right">0.0916</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">1.410227</td>
## <td class="gt_row gt_right">0.24</td></tr>
## </tbody>
##
## <tfoot class="gt_footnotes">
## <tr>
## <td class="gt_footnote" colspan="8"><sup class="gt_footnote_marks gt_asterisk">***</sup> p < 0.001</td>
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##
## [[2]]
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## <thead class="gt_header">
## <tr>
## <th colspan="5" class="gt_heading gt_title gt_font_normal" style>Tukey test</th>
## </tr>
## <tr>
## <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
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## <thead class="gt_col_headings">
## <tr>
## <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Estimate</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Z ratio</th>
## <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">p</th>
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## <tbody class="gt_table_body">
## <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - EQ<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #FBC28B; color: #000000;">0.0301</td>
## <td class="gt_row gt_right">0.0067</td>
## <td class="gt_row gt_right">4.4781</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.2 × 10<sup class='gt_super'>−5</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## <tr><td class="gt_row gt_left">EG - R</td>
## <td class="gt_row gt_right" style="background-color: #E5E1FD; color: #000000;">−0.0087</td>
## <td class="gt_row gt_right">0.0067</td>
## <td class="gt_row gt_right">−1.2978</td>
## <td class="gt_row gt_right">0.396384</td></tr>
## <tr><td class="gt_row gt_left" style="font-weight: bold;">EQ - R<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #8787FC; color: #000000;">−0.0388</td>
## <td class="gt_row gt_right">0.0067</td>
## <td class="gt_row gt_right">−5.7761</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.3 × 10<sup class='gt_super'>−8</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
## </tbody>
##
## <tfoot class="gt_footnotes">
## <tr>
## <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p < 0.001</td>
## </tr>
## </tfoot>
## </table>
## </div>
rda_ind <- format_rda(here(p3path, "rda_indsampling_results.csv"))
rda_ind_tidy <-
rda_ind %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
group_by(correctPC) %>%
group_split()
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
rda_ind <-
rda_ind %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
filter(correctPC == "FALSE")
run_lmer(rda_ind, "TPRCOMBO", filepath = here(p4path, "RDA_individual_TPR.csv"))
[[1]]
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | 0.0002 | 2.8394 | 2.8394 | 1 | 15.3480K | 545.389450 | 1.5 × 10−118*** |
| sampstrat | 0.0875 | 0.3001 | 0.1000 | 3 | 15.3480K | 19.211563 | 2.0 × 10−12*** |
| K | 0.0165 | 1.0439 | 1.0439 | 1 | 15.3480K | 200.509665 | 3.1 × 10−45*** |
| m | 0.0438 | 7.3555 | 7.3555 | 1 | 15.3480K | 1412.856406 | 7.2 × 10−296*** |
| phi | 0.0440 | 7.4213 | 7.4213 | 1 | 15.3480K | 1425.494641 | 2.2 × 10−298*** |
| H | 0.0436 | 7.2900 | 7.2900 | 1 | 15.3480K | 1400.274445 | 2.3 × 10−293*** |
| r | 0.0036 | 0.0488 | 0.0488 | 1 | 15.3480K | 9.371404 | 2.2 × 10−3** |
| *** p < 0.001 | |||||||
| ** p < 0.01 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G | 0.0005 | 0.0016 | 0.2768 | 0.9926010 |
| EG - R | 0.0029 | 0.0016 | 1.7594 | 0.2931233 |
| EG - T*** | 0.0110 | 0.0016 | 6.6817 | 1.4 × 10−10*** |
| G - R | 0.0024 | 0.0016 | 1.4826 | 0.4480091 |
| G - T*** | 0.0105 | 0.0016 | 6.4050 | 9.0 × 10−10*** |
| R - T*** | 0.0081 | 0.0016 | 4.9224 | 5.1 × 10−6*** |
| *** p < 0.001 | ||||
run_lmer(rda_ind, "FDRCOMBO", filepath = here(p4path, "RDA_individual_FDR.csv"))
[[1]]
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | 0.0003 | 5.7961 | 5.7961 | 1 | 15.3480K | 373.268676 | 3.4 × 10−82*** |
| sampstrat | 0.1162 | 0.2103 | 0.0701 | 3 | 15.3480K | 4.515102 | 3.6 × 10−3** |
| K | 0.0153 | 0.9004 | 0.9004 | 1 | 15.3480K | 57.987784 | 2.8 × 10−14*** |
| m | 0.0753 | 21.8007 | 21.8007 | 1 | 15.3480K | 1403.969867 | 4.2 × 10−294*** |
| phi | 0.0647 | 16.0600 | 16.0600 | 1 | 15.3480K | 1034.264854 | 1.2 × 10−219*** |
| H | 0.0610 | 14.2799 | 14.2799 | 1 | 15.3480K | 919.628150 | 3.1 × 10−196*** |
| r | 0.0091 | 0.3176 | 0.3176 | 1 | 15.3480K | 20.451012 | 6.2 × 10−6*** |
| *** p < 0.001 | |||||||
| ** p < 0.01 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - G | −0.0010 | 0.0028 | −0.3555 | 0.98460216 |
| EG - R | 0.0020 | 0.0028 | 0.6959 | 0.89870855 |
| EG - T*** | 0.0085 | 0.0028 | 2.9888 | 0.01487071*** |
| G - R | 0.0030 | 0.0028 | 1.0514 | 0.71907362 |
| G - T** | 0.0095 | 0.0028 | 3.3443 | 4.6 × 10−3** |
| R - T | 0.0065 | 0.0028 | 2.2929 | 0.09963697 |
| *** p < 0.05 | ||||
| ** p < 0.01 | ||||
MEGAPLOT(rda_ind, "TPRCOMBO", colpal = "plasma")
MEGAPLOT(rda_ind, "FDRCOMBO", colpal = "viridis", direction = -1)
MEGAPLOT(rda_ind, "TOTALN", colpal = "viridis")
rda_site <- format_rda(here(p3path, "rda_sitesampling_results.csv"))
rda_site_tidy <-
rda_site %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
group_by(correctPC) %>%
group_split()
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
walk(TOTALN_plots, grid.arrange)
rda_site <-
rda_site %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
filter(correctPC == "FALSE")
run_lmer(rda_site, "TPRCOMBO", filepath = here(p4path, "RDA_site_TPR.csv"))
[[1]]
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | 0.0015 | 0.8335 | 0.8335 | 1 | 8.6290K | 232.154396 | 9.5 × 10−52*** |
| sampstrat | 0.0717 | 0.1133 | 0.0567 | 2 | 8.6290K | 15.782322 | 1.4 × 10−7*** |
| K | 0.0173 | 0.6489 | 0.6489 | 1 | 8.6290K | 180.732574 | 8.6 × 10−41*** |
| m | 0.0322 | 2.2403 | 2.2403 | 1 | 8.6290K | 623.983518 | 5.0 × 10−133*** |
| phi | 0.0321 | 2.2322 | 2.2322 | 1 | 8.6290K | 621.743005 | 1.4 × 10−132*** |
| H | 0.0315 | 2.1447 | 2.1447 | 1 | 8.6290K | 597.363316 | 1.3 × 10−127*** |
| r | 0.0019 | 0.0081 | 0.0081 | 1 | 8.6290K | 2.261166 | 0.13 |
| *** p < 0.001 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ | −0.0001 | 0.0016 | −0.0550 | 0.9983351 |
| EG - R*** | 0.0076 | 0.0016 | 4.8378 | 3.9 × 10−6*** |
| EQ - R*** | 0.0077 | 0.0016 | 4.8928 | 3.0 × 10−6*** |
| *** p < 0.001 | ||||
run_lmer(rda_site, "FDRCOMBO", filepath = here(p4path, "RDA_site_FDR.csv"))
[[1]]
| Linear mixed effect model | |||||||
|---|---|---|---|---|---|---|---|
| statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed) | |||||||
| Predictors | Fixed Effects | Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) |
| nsamp | 0.0018 | 1.1681 | 1.1681 | 1 | 8.6290K | 140.00975 | 4.7 × 10−32*** |
| sampstrat | 0.0845 | 0.1085 | 0.0542 | 2 | 8.6290K | 6.50242 | 1.5 × 10−3** |
| K | 0.0133 | 0.3801 | 0.3801 | 1 | 8.6290K | 45.55864 | 1.6 × 10−11*** |
| m | 0.0378 | 3.0791 | 3.0791 | 1 | 8.6290K | 369.07182 | 1.4 × 10−80*** |
| phi | 0.0336 | 2.4370 | 2.4370 | 1 | 8.6290K | 292.10683 | 2.0 × 10−64*** |
| H | 0.0297 | 1.8994 | 1.8994 | 1 | 8.6290K | 227.67214 | 8.5 × 10−51*** |
| r | 0.0144 | 0.4449 | 0.4449 | 1 | 8.6290K | 53.32587 | 3.1 × 10−13*** |
| *** p < 0.001 | |||||||
| ** p < 0.01 | |||||||
| Tukey test | ||||
|---|---|---|---|---|
| pairwise ~ sampstrat | ||||
| Contrast | Estimate | SE | Z ratio | p |
| EG - EQ*** | 0.0057 | 0.0024 | 2.3728 | 0.04642683*** |
| EG - R** | 0.0085 | 0.0024 | 3.5382 | 1.2 × 10−3** |
| EQ - R | 0.0028 | 0.0024 | 1.1654 | 0.47395300 |
| *** p < 0.05 | ||||
| ** p < 0.01 | ||||
MEGAPLOT(rda_site, "TPRCOMBO", colpal = "plasma")
MEGAPLOT(rda_site, "FDRCOMBO", colpal = "viridis", direction = -1)
MEGAPLOT(rda_site, "TOTALN", colpal = "viridis")
arrange_figures(lfmm_ind, rda_ind, "FDR",
"A. LFMM", "B. RDA",
colpal = "viridis", direction = -1, dig = 2, maxv = 0.86, minv = 0)
arrange_figures(lfmm_ind, rda_ind, "TPR",
"A. LFMM", "B. RDA",
colpal = "plasma", direction = 1, dig = 2, minv = 0, maxv = 0.17)
arrange_figures(lfmm_site, rda_site, "TPR",
"A. LFMM", "B. RDA",
colpal = "plasma", direction = 1, dig = 2, minv = 0, maxv = 0.11)
arrange_figures(lfmm_site, rda_site, "FDR",
"A. LFMM", "B. RDA",
colpal = "viridis", direction = -1, dig = 2, maxv = 1, minv = 0)